Setup

Background

Datasets

Ramakar et al (2017)

  • Selection of metadata variables for subset

##                                                        V1
## RunID                                         -0.92207331
## SampleID                                       0.56588402
## SampleACC                                      0.52187022
## ExperimentACC                                  0.52227248
## ExperimentTitle                                0.52227248
## SampleAttributes                              -0.72217656
## ExperimentAttributes                           0.52227248
## SampleName                                     0.52227248
## SampleTitle                                   -1.23951411
## SampleBases                                    1.12469750
## SampleSpots                                    1.12469750
## RunPublished                                   0.55583963
## Size                                           1.13646420
## RunTotalBases                                  1.12469750
## RunTotalSpots                                  1.12469750
## NumSpots                                       1.12469750
## ReadInfo                                       0.39151818
## RunAlias                                       0.56588402
## ChimericPairs                                  0.01401913
## Percent_aligned_ChrX                          -1.10900870
## Percent_aligned_ChrY                          -1.22596746
## AUC_all_alignments                             1.16003963
## AUC_all_annotated_exons                        1.15464673
## AUC_uniquely_aligned                           1.15450709
## AUC_all_annotated_exons_unique                 1.15267282
## AUC_all_percentage                            -0.20375605
## AUC_unique_percentage                         -0.32956490
## TotalNFragments                                1.15974100
## ReadFragmentLength                             1.16334602
## MeanFragmentLength                            -0.74930177
## MeanFragmentLength_BAM                        -1.44864053
## ModeFragmentLength                            -1.36344896
## ModeFragmentLengthCount                        0.98793867
## Percentage_fragment_mapped_exon_fc            -0.82778239
## Percentage_fragment_mapped_unique_exon_fc     -0.92522176
## Total_fragments_input_fc_exon_fc               1.15700790
## Total_fragments_assigned_exon_fc               1.08295864
## Total_fragments_count_unique_exon_fc           1.15700790
## Total_fragments_count_unique_assigned_exon_fc  1.08295864
## Percentage_fragment_mapped_gene_fc            -0.75947235
## Percentage_fragment_mapped_unique_gene_fc     -0.88428933
## Total_fragments_input_fc_gene_fc               1.15700790
## Total_fragments_assigned_gene_fc               1.09171621
## Total_fragments_count_unique_gene_fc           1.15700790
## Total_fragments_count_unique_assigned_gene_fc  1.08145691
## IntronTotal                                    0.71789243
## IntronicRate                                  -0.89706236
## Percentage_chimeric_reads_STAR                -0.59599104
## Percentage_mapped_multi_loci_STAR             -1.08002420
## Percentage_mapped_too_many_loci_STAR          -0.82344064
## Percentage_unmapped_other_STAR                -0.57569697
## Percentage_unmapped_too_short_STAR            -1.87378200
## ReadsMapped                                    1.15974100
## Average_mapped_length_STAR                    -0.31376005
## Deletion_average_length_STAR                  -0.54905080
## Deteltion_rate_per_base_STAR                  -0.29299586
## Insertion_average_length_STAR                 -0.54415312
## Insertion_rate_per_base_STAR                  -1.51015141
## Mapping_speed_per_hour_STAR                   -0.95678448
## Percentage_mismatch_per_base_STAR             -1.73177086
## Number_of_chimeric_reads_STAR                  1.10762237
## TotalNReads                                    1.12469750
## Number_reads_mapped_to_multiple_loci_STAR      0.95868089
## Number_reads_mapped_to_too_many_loci_STAR      0.81135118
## Number_reads_unmapped_other_STAR               0.52753358
## Number_reads_unmapped_too_short_STAR          -0.52434834
## Number_canonical_splices_AT_AC_STAR            0.74891267
## Number_canonical_splices_GC_AG_STAR            0.77264527
## Number_canonical_splices_GT_AG_STAR            0.77206646
## Number_non_canonical_splices_STAR              1.03569281
## Number_splices_total_STAR                      0.77455521
## MappingRate                                   -0.25005180
## MappingRate_unique                             1.15417303
## Junction_count                                 0.70888310
## Junction_coverage                              0.78152832
## Junction_average_coverage                      0.69608728
## Number_input_reads_both_STAR                   1.12469750
## All_mapped_reads_both_STAR                     1.15974100
## Number_chimeric_reads_both_STAR                1.10762237
## Number_reads_mapped_multiple_loci_both_STAR    0.95868089
## Numner_reads_mapped_too_many_loci_both_STAR    0.81135118
## Number_reads_unmapped_other_both_STAR          0.52753358
## Number_reads_unmapped_too_short_both_STAR     -0.52434834
## Number_reads_mapped_uniquely_both_STAR         1.15417303
## MappingRate_both                              -0.30067430
## Percent_Chimeric_both                         -0.59525170
## Percentage_mapped_multi_loci_both_STAR        -1.07919545
## Percentage_mapped_too_many_loci_both_STAR     -0.77900075
## Percentage_unmapped_other_both_STAR           -0.71156482
## Percentage_unmapped_too_short_both_STAR       -1.87393185
## Percentage_uniquely_mapped_both_STAR          -0.24988415
## DIstinctQualityValues                         -0.38163684
## Percent_Bases                                  1.12469750
## Percent_A                                      0.32372534
## Percent_C                                     -2.26309208
## Percent_G                                     -2.29141772
## Percent_T                                      0.16873923
## Percent_N                                     -1.64022797
## Average_Phred                                 -0.33017200
## ErrQ                                          -0.50054673
## SampleAccPrediction                            0.52187022
## PredictionType                                -1.85518724
## BigWigFile                                    -1.23564405
## Age                                           -0.73338606
## pH                                            -0.98860509
## StructureAcronym                              -1.05218257
## Diagnosis                                     -1.02821128
## Ethnicity                                     -0.70033387
## Sex                                           -1.28230304
## PMI                                           -1.02004084
## Regions                                       -1.07465807
## Age_rounded                                   -0.73338606
## AgeInterval                                   -0.74480077
  • Selection for variance Partition
OriginalMetadataColumnName BITColumnName Type
external_id SampleID Sample charactertics
sra.run_total_spots RunTotalSpots Sequencing metrics
recount_qc.aligned_reads..chrm ChimericPairs Sequencing metrics
recount_qc.aligned_reads..chrx Percent_aligned_ChrX Sequencing metrics
recount_qc.aligned_reads..chry Percent_aligned_ChrY Sequencing metrics
recount_qc.bc_auc.all_reads_all_bases AUC_all_alignments Sequencing metrics
recount_qc.bc_auc.unique_reads_all_bases AUC_uniquely_aligned Sequencing metrics
recount_qc.bc_auc.all_. AUC_all_percentage Sequencing metrics
recount_qc.bc_auc.unique_. AUC_unique_percentage Sequencing metrics
recount_qc.bc_frag.count TotalNFragments Sequencing metrics
recount_qc.bc_frag.mode_length_count ModeFragmentLengthCount Sequencing metrics
recount_qc.exon_fc.all_. Percentage_fragment_mapped_exon_fc Sequencing metrics
recount_qc.exon_fc.unique_. Percentage_fragment_mapped_unique_exon_fc Sequencing metrics
recount_qc.exon_fc_count_all.total Total_fragments_input_fc_exon_fc Sequencing metrics
recount_qc.exon_fc_count_all.assigned Total_fragments_assigned_exon_fc Sequencing metrics
recount_qc.exon_fc_count_unique.total Total_fragments_count_unique_exon_fc Sequencing metrics
recount_qc.exon_fc_count_unique.assigned Total_fragments_count_unique_assigned_exon_fc Sequencing metrics
recount_qc.gene_fc.all_. Percentage_fragment_mapped_gene_fc Sequencing metrics
recount_qc.gene_fc.unique_. Percentage_fragment_mapped_unique_gene_fc Sequencing metrics
recount_qc.gene_fc_count_all.total Total_fragments_input_fc_gene_fc Sequencing metrics
recount_qc.gene_fc_count_all.assigned Total_fragments_assigned_gene_fc Sequencing metrics
recount_qc.gene_fc_count_unique.total Total_fragments_count_unique_gene_fc Sequencing metrics
recount_qc.gene_fc_count_unique.assigned Total_fragments_count_unique_assigned_gene_fc Sequencing metrics
recount_qc.intron_sum IntronTotal Sequencing metrics
recount_qc.intron_sum_. IntronicRate Sequencing metrics
recount_qc.star.._of_reads_mapped_to_multiple_loci Percentage_mapped_multi_loci_STAR Sequencing metrics
recount_qc.star.._of_reads_mapped_to_too_many_loci Percentage_mapped_too_many_loci_STAR Sequencing metrics
recount_qc.star.._of_reads_unmapped._other Percentage_unmapped_other_STAR Sequencing metrics
recount_qc.star.._of_reads_unmapped._too_many_mismatches Percentage_unmapped_too_many_mismatches_STAR Sequencing metrics
recount_qc.star.._of_reads_unmapped._too_short Percentage_unmapped_too_short_STAR Sequencing metrics
recount_qc.star.all_mapped_reads ReadsMapped Sequencing metrics
recount_qc.star.number_of_input_reads TotalNReads Sequencing metrics
recount_qc.star.uniquely_mapped_reads_. MappingRate Sequencing metrics
recount_qc.star.uniquely_mapped_reads_number MappingRate_unique Sequencing metrics
recount_qc.junction_count Junction_count Sequencing metrics
recount_qc.junction_coverage Junction_coverage Sequencing metrics
recount_qc.junction_avg_coverage Junction_average_coverage Sequencing metrics
recount_qc.star.number_of_input_reads_both Number_input_reads_both_STAR Sequencing metrics
recount_qc.star.all_mapped_reads_both All_mapped_reads_both_STAR Sequencing metrics
recount_qc.star.._mapped_reads_both MappingRate_both Sequencing metrics
recount_qc.star.._reads_mapped_to_multiple_loci_both Percentage_mapped_multi_loci_both_STAR Sequencing metrics
recount_qc.star.._reads_mapped_to_too_many_loci_both Percentage_mapped_too_many_loci_both_STAR Sequencing metrics
recount_qc.star.._reads_unmapped._other_both Percentage_unmapped_other_both_STAR Sequencing metrics
recount_qc.star.._reads_unmapped._too_many_mismatches_both Percentage_unmapped_too_many_mismatches_both_STAR Sequencing metrics
recount_qc.star.._reads_unmapped._too_short_both Percentage_unmapped_too_short_both_STAR Sequencing metrics
recount_qc.star.uniquely_mapped_reads_._both Percentage_uniquely_mapped_both_STAR Sequencing metrics
NA Age Phenotype
NA pH Sequencing metrics
NA StructureAcronym Sample charactertics
NA Diagnosis Phenotype
NA Ethnicity Phenotype
NA Sex Phenotype
NA PMI Sequencing metrics
NA Regions Sample charactertics
NA Period Phenotype
NA AgeInterval Phenotype